A Spartan and a Spectre
by W0lfsimien
Summary: Following the battle of the arc our favorite spartan finds himself in a different Milky Way, with a whole new enemy to fight. Commander Shepard, Hero of Elysium, on a standard snatch and grab mission suddenly finds a strange man in with stranger weapons and armor, and a new enemy more dangerous than any she could even imagine. A reboot of my previous story.
1. Chapter 1

**A Spartan and a Spectre**

(Disclaimer) I own neither Halo any of its characters or Mass effect or any of its characters. they belong to 343 Industries and Bioware. Pretty much everything below here is their work

'Charging sequence 90%, firing sequence initiating, hurry up Chief!'Cortana almost screamed from panic.

John cranked the steering wheel, sending his Warthog into a sharp turn, suppressing a feeling of panic as the vehicle tilted precariously on two wheels before it slammed back onto the ground and shot forward bringing the dawn into sight. Swerving occasionally to avoid the ever present and dangerous sentinels, the Arbiter sending a steady stream of fire towards any that came too close.

As the Dawn came closer Chief felt the steering wheel crack in his hands before he could force his nerve tense muscles to relax

'Gun it Chief, jump!, right into the hanger!' Cortana yelled as they neared the gap, missing the fact that John had already flattened the petal from slamming it down on the floor board.

They hit a ramp, sending the trio over a small gap leading into the recesses of the exploding station, then the vehicle was across the gap slamming into the deck of the frigate throwing its occupants out..

_'you're not done yet.' _Chief told himself forcing himself up as every bruise and burn he endured that day seemed to flare up at once. The Spartan just managed to get to his hands and knees when the ship lurched from the exploding station, nearly sending him back to the floor. Head snapping forward, energized by the reminder of his situation, he started to push himself up when he saw the arbiter out of the corner of his eye jump behind a stack of crates, followed by a scorpion tank.

Moving past the overturned vehicle that carried them to their only chance of safety, John spared a glance at the stack of crates in time to see his Sangheili ally extract himself relativity unharmed. A quick nod between the two and the Spartan made his way towards the hangars holographic podium pushing Cortana's chip in as hard as he dared without breaking it, While the Arbiter made his way to a hallway leading to the brige.

"Hang on!." Cortana called out, as she started the Dawns engines, sending a rumble through the ship as it started moving. John held tightly to the podium as gravity tried to drag him out the hanger door

People often call Chief lucky, in fact it was one of the reasons Cortana chose him.

_'Crash'_

As a near miss from a falling warthog knocked him from the podium, he began to wonder if that legendary luck had finally run out..

Chief managed to make a handhold onto the floor, when a scorpion tank soared over him out the hanger door.

Chief watched the armored vehicle the armored vehicle that so narrowly missed him. That would have crushed him had he stopped himself so much as half a second before or after, and turned back to the terminal holding Cortana and started pulling himself up making his way to his friend

The soldier pulled himself to his feet sparing a brief look at his diminutive partner and pulled out her chip before making his way to the far end of the terminal  
'Chief... in case we don't make it...' Cortana tried to say to the super soldier after he plugged her chip into his helmet.  
'We'll make it.' He interrupted in his usual gravelly voice, sounding as if it was already guarenteed.  
'Its been an honer to serve with you john.' The A.I. finished  
Suddenly the ship lurched forward pressing Chief into the terminal, followed by a blinding white light before fading into black as he lost conciseness."

* * *

'Chief?...'

Pain...

'Chief?...'

Pain always seemed to be the first thing Chief felt when he woke up, and this pain was particularly bad after the hits Guilty Spark gave him. With a second of focus he shoved the pain away and opened his eyes to the image of an upside down frigate hanger, along with the familiar disorientation of weightlessness..

'Chief can you hear me?!' a familiar voice called bringing his attention to the present,and with a thought he turned on his helmet light.

'Oh thank goodness. I thought I lost you too.' His partner sighed in relief as he reoriented himself, grabbed his rifle and pushed himself towards the hanger exit. If they were drifting through space, there was only one thing he could do.

'What happened?' he asked his digital partner, silently worrying about how she would handle the foreseeable future.

'I don't know.' She responded, before musing out loud. 'The Halo shook itself to pieces, must have done a number on the Ark. The portal couldn't sustain itself. We made it thorugh just in time... Well part of us anyway.' She finished as they passed a damaged section of the ship showing the empty void of space broken only by the distant glimmer of the stars.

'But you did it' She said, trying to sound optimistic, as they entered the cryo-bay. 'Truth, the Covenant, the Flood, it's finished.'

'It's finished.' John agreed, removing her chip from his helmet, and placing it into a holo-terminal.

'I'll drop a beacon, but It'll be a while before anyone finds us.' Cortana said quietly, watching as the soldier put his rifle on a weapons rack, and moved to the nearest tube.

'Wake me, when you need.' he said, laying back in the pod, taking one last solemn look at his friend before closing his eyes, for the wait to come as the pod hissed shut.

* * *

(Councilor Udina, Captain Anderson, And Admiral Hackett discussing Specter candidates.)  
Udina: Well what about Shepard, she grew up in the colonies.  
Anderson: She knows how tough life can be out there, her parents were killed during the slaver attack on mindoir.  
Hackett: She proved herself in the Blitz, held off enemy forces on the ground until reinforcements arrived.  
Anderson: She's the only reason Elysium is still standing.  
Udina: We can't question her courage.  
Anderson: Humanity needs a hero, and Shepard's the best we got.  
Udina: I'll make the call.

* * *

(Normandy)

The SSV Normandy, The most advanced warship in the galaxy, with the new, highly secret, stealth technology and and extra the large Tantalus drive core made it one of the fastest and most dangerous ships in the galaxy. A cooperative effort between some of the best scientists between the Human systems alliance and the Turian Hierarchy.

"_With everything they put into this ship, they couldn't install a faster lift." _Thought the current user of said lift, famous Naval Lieutenant Commander Kaine Shepard hero of Elysium, and to those who served on board the second in command of the ship.

After a seeming eternity to the woman inside, the door finally opened in time for the ships pilot to call out preparations for its first official relay jump.

'Arcturus prime relay is in range, initiating transmission sequence.' joker announced over the com, for the warships first jump.

The Alliance Vanguard made her way up the stairs leading to the CIC, and made her way to the ships cockpit; the pilot announcing jump procedures over the ship radio

'Board is green, approach run has begun.' Joker called out as the Commander stopped behind the pilots chair. With a glance to the Turian Spectre watching over the ships test run. 'Hitting the relay in 3... 2... 1.' Joker called out, and Shepard saw the universe blink as they crossed several light years in an instant.

'Thrusters... Check, Navigation... Check, Internal emissions sink engaged, all systems online, drift... just under 1500K.' joker announced after the jump.

'1500 is good, your captain will be pleased.' Nihilus announced in approval as he turned away, his official reason for being on the ship complete.

'I hate that guy.' The Pilot stated succinctly, sending a quick scowl at the retreating back of the turian.

'Nihilus gave you a compliment so you hate him?' Staff Lieutenant Kaiden Alenko asked, an amused smile stretching his mouth at the pilots antics.

'Remember to zip up your jumpsuit after using the bathroom, that's good I just jumped us half way across the galaxy, and hit a target the size of a pinhead, so that's incredible.' joker shot back. 'Besides Specters are trouble, I don't like having one of them on board, call me paranoid.'

'Your paranoid.' Kaiden agreed. 'The Council helped fund this project, they have a right to send someone to keep an eye on their investment.'

'So they send a spectre?' Kaine cut in. 'For a test run the usual overseer is an officer. Or I don't know maybe an engineer to make sure everything is running smoothly, not a special operative. And why do we have a full crew, for a test run like this procedure is to use a skeleton crew.' She continued, now musing aloud.

'So you agree with me something isn't right' Joker laughed in victory when the captains voice barked over the radio. '**Joker Status report.'**

'Just cleared the mass relay, stealth systems engaged, everything is solid.' Joker snapped off, back going straight as if the captain were in the cabin with them. '**Good find a com-bouy hook us into the system.'** Anderson ordered. '**I want a mission report relayed to the brass before we reach the colony.'  
'Aye aye Captain.' **Joker said. 'Better brace yourself, I think Nihilus is on his way to you.'

'He is already here.' Captain Anderson said in exasperation. 'Send the commander to the comm room, I need to speak with her.'

'Yeah great, I think you just Pissed him off'. Kaine said as she turned to walk to the comm room.

'Don't blame me.' Joker said defensively. 'He always sounds angry.'

'Only when he's talking to you.' Kaiden claimed, sounding distracted a small part of her noticed.

* * *

With her orders, Shepard left her compatriots in the cockpit, and made her way through the CIC, only paying enough attention on her path to get to her destination without running into anything or anyone. Mind lost in a mental search for the true purpose of the Normandy's maiden voyage, until an over eager voice broke her out of any further musings.

'What do you think commander, we won't be staying on the ground too long, I want a chance to see some real action.'

Blinking in surprise, the commander turned to find a fresh faced private looking at her expectantly. Mentally going through the crew manifest she was given when she was assigned to the Normandy, she managed to pull a name from the foggier corners of her mind, A private R something... Richard... Richard Jenkins. Before She could think of a response however, A stern looking woman with a matronly face; which Shepard had a much easier time putting a name to, Normandy's Chief Medical Officer Dr. Chakwas, spoke up.

'I sincerely hope you're joking, your real action usually leaves me patching people up in the infirmary.'

'Ahhh' Kaine mouthed silently as the turned their attention back to each other, guessing the nature of their previous conversation. 'Jenkins Right?' Shepard asked, drawing twos attention back to her.

'Yes Ma'am.' the private affirmed seeming to stand straighter when she said his name.

'Now I'm guessing you're looking for a chance to prove yourself, show what you can do.'

'Well... Well yeah, it's... It's just that you proved yourself at Elysium. And Nihilus is a Spectre, everyone knows what he can do. And well I grew up on Eden Prime, and nothing really happens there.'

'Then listen, you're young, if your smart you can have a long career ahead of you. Whatever happens, the best thing you can do is keep a cool head.'

The young private frowned at her response for a second. 'Sorry Commander, but we actually have a Spectre with us.'

'Stop!...' Jenkins flinched in surprise at her snapping at him, giving his superior his full attention. 'It doesn't matter who is with us, Like I told you keep a cool head, treat this like any other mission and you will do fine.'

'yes ma'am.' The private saluted, to which the commander nodded, and started to turn away, until a thought occurred to her. 'Jenkins, you said you grew up on Eden Prime, can you tell me anything about it?'

'Sure, but it's pretty much the same as they say in the Vids. It's really peaceful, and they were careful with development to minimize pollution. I grew up on the outskirts, at night I would climb up this tall hill and stare at the city. But after a while I realized it was all a little too quiet for me. Heh... Even paradise gets boring after a while.'

'I see...' Kaine mused quietly to herself. '_In other words a perfect place to test out the new stealth system. So no clues from the location itself.' _She thought wryly.  
'And can either of you tell me anything about Nihilus?'

'You mean besides the fact that he's one of the Biggest badasses in the galaxy.' Jenkins exclaimed excitedly, getting ready to rant as only a fanboy can; when butted in saving her from the tangent.  
'Not much I'm afraid, He spends most of his time with the Captain.'

At the mention of the C-word, Shepard was reminded of her standing orders to meet him, and with a quick goodbye she rushed to the thankfully nearby doors to the comms-room.

Inside she found the source of much of the ships intrigue, standing alone,with no Captain or anyone else, in utter solitude until she showed up. While some part of her mind went on to list how alone he was, the Turian Spectre turned to her. 'Ah Shepard good, I was hoping for a chance to speak to you alone.'

"Right, and I thought Captain Anderson was supposed to be here." Stated Kaine warily, a dark part of her mind wondering if the door closing sounded more ominous than usual. '_Nah, probably just too many late night horror vids.'_

'He's on his way.' The Spectre stated dismissivly. 'Now I was wondering what you could tell me about this world we're visiting. Eden Prime, It's supposed to be very peaceful.'

'I can't say I've ever been there, but from what I've heard it's supposed to be a paradise.' The N7 operative answered slowly, mentally dissecting the question for any double meanings.

'Yes a paradise, proof that not only can humans build colonies across the galaxy, but also protect them. But how safe are they really,'

'Are you trying to insinuate something.' Kaine replied coldly leveling a glare at the Turian Spectre... which only served to amuse the avian alien.

'Not at all, I'm merely pointing out that the galaxies a vast place, and there is much we still don't know about it. And who knows how many dark secrets it has.'

Kaine opened her mouth to argue for the Alliance when a familiar voice deep spoke up behind her.

'I believe it's time we told Shepard the Truth.' The Commander turned to her Captain raising an inquisitive eyebrow, when Nihilus spoke up beside her.'This mission is far more than a simple shakedown run.'

"Oh you don't say." Kaine muttered sardonically.

Which Anderson proceeded to ignore. "'A recent excavation project has unearthed some kind of beacon. We believe it is Prothean in origin,' At that information Kaine's eyes widened. 'Now I know I don't need to tell you what that means for the Galaxy, let alone Humanity. So when we get to Eden Prime we're going to go in quiet and get out with as few people knowing as possible, understood.'

'Just one thing sir. Why all the secrecy?' Kaine asked slowly. ' I mean Eden Prime is deep in alliance territory, not even the Batarians would attack this deep.'

Anderson nodded his head in understanding, his face a blank mask. 'Ordinarily you would be right, but for something like this... Well it's best not to to take any chances.' Shepard nodded letting the Captain continue. 'This is about more than the Beacon, it's also about you.'

The Alliance Vanguard blinked in surprise. 'Uhh... Okay...' Kaine responded slowly, giving the two a long look, as her mind started putting the pieces together. 'So... You want to make me a Spectre?'

Anderson nodded managing to look both proud and sympathetic. While Kaine started wondering how he managed that, the Captain started explaining. 'The Alliance has been pushing for this for a long time, Humanity wants a larger role in shaping galactic policy, we want more say with the Citadel Council. Nihilus here has agreed to evaluate you for the Position.'

'I was under the impressions that Turians didn't trust Humanity, so why would you agree to this?' Kaine asked.

'I read the report on Elysium, you displayed many skills there necessary for a Spectre.' The Council agent explained. 'We don't all hate Humans, some of us see the good you can do. And going by your service record you may be just what we need,'

'Uh. Understood.' Kaine replied unconsciously standing straighter at the agents praise.

'Good.' Anderson announced, now in full command mode. "Now when we get ground side..."

**'Captain we have a problem.'** Jokers voice cut in over the comms.

'What is it Joker.'

**'Transmission from Eden Prime sir... You better see this.'**

After the Normandy pilots announcement, the room darkened and a screen came up on the back wall, playing the shaking footage of a soldiers helmet camera. The sound of gunfire started playing over the speakers. The video showed a vicious ground battle. An alliance marine showed up in front of the camera.  
'We are under attack, Taking heavy casualties. I repeat heavy casualties.' The Marine officer sounded increasingly panicked over the video until a loud noise loud noise, almost a roar came out of the speakers. The shooting in the background slowed and stopped as everyone including the owner of the helmet stopped and looked up. A giant ship that looked almost like a hand was descending, like it was reaching down to crush the defenders. The screen faded to static. '**Everything cuts out after that, no com traffic at all. Just goes dead.'** Joker declared solemnly.

Anderson studied the screen, a curious look on his face. 'Reverse and hold at 38.5' He ordered, watching as the screen showed the strange ship appeared on the screen again. Kaine fought the urge to step back, something about the ship seemed very wrong to her. Anderson spoke up again. 'Joker status report.'

**'Seventeen minutes out. No other Alliance ships in the area.'**

Anderson took a deep breath, and opened his mouth to say something, when Lieutenant Alenko spoke up over the com.  
'**Wait, Captain I think I've found something, an unknown signal, I can't where it's coming from though.'**

The three in the room shared a look, Anderson spoke up. 'Joker you said there was no other com traffic in the system.'

**'I know sir, but the signal is faint, we're barely getting it as is. I don't even know how he picked it up.' **The last part came out over the radio.

'What was that Joker.' The captain called out irate, before giving a small sigh.

**'Uhh... Just saying that I can't find a match for the signal in our database and it seems to be to garbled to translate... wait I think I got something.'**

A female voice came out of the Speakers, occasionally broken by static. 'Mayday Ma- UNSC FFG Forward Unto Da-diate Evac, Surv- Prio- Victo- 3 Sierra 1.1.7'

The three shared a look. 'That was definitely English, A human language.' Nihilus mused sending a searching look to the Alliance officers.

Shepard's mind was racing trying to make sense of the message, She started musing aloud. 'I never heard of any UNSC, or that kind of ship classification either.'

Anderson looked at the now blank screen thoughtfully for a few seconds. 'Our mission is the Beacon, we can look into this strange signal after it's secure.'

Kaine expected some kind of complaint from the Turian Spectre, instead he just nodded in agreement. '_Right' _She thought. _'Professional, mission first.' _Kaine looked back at the blank screen. 'A distress signal, not to different from standard. Probably nothing as interesting as a Prothian beacon anyway.'

(A/N) I Hope you enjoy the reboot.


	2. Isolation

(A/N) So let me start by apologizing about any confusion I may have caused in my last update. That statement was not meant to be taken seriously, which I had hoped to confer by adding a link to this new story, clearly I failed so to anyone I may have confused and/or offended I am sorry.

That done, here is what I'm calling chapter 0.5. It will probably answer none of your questions. Enjoy

**Isolation**

It started slowly.

Cortana watched the hatch on the Cryo-chamber close, the Chiefs last words echoing in her mind, the long wait for help looming before her.

At first she tried to keep busy, but being a body less A.I in half a ship her options were limited. She found a small supply of experimental nanomachines, ONI tech, probably taken during the quick supply before the ships left for the ARC. The work with them was slow, but largely autonomous; the main issue was how long they would last. She would start them on the inside, focusing on the inner mechanisms of the armor, and work her way out, she just had to check on them between each project and limit the working speed if she was to have any hope of finishing.

Unfortunately the inevitable happened and Cortana soon found herself out of busy work. While she was still working on Chiefs armor, the project required little of her attention, and she soon found herself with nothing else to pass the time.

All the seconds...

Minutes...

Hours...

Days...

Months...

Years... She kept herself busy any way she could, increasingly complex math problems, going over past missions with John, reviewing data she acquired from Forerunner systems, anything she could do .

She was logging the latest day adrift when it happened.3 years 7 months 6 days since the portal shot them to unknown sectors of space. UEG date Capitol on earth... 2556 June _. Cortana froze unable to remember the day. Fear surging through her she sent a scan through her systems and found a small run time error, a quick and simple fix. A human would never notice the delay, but Cortana knew what it meant. She remembered her time with the Gravemind, a taste of the storm to come.

* * *

3 Years 9 Months 15 Days

Cortana was watching her last mission, Guilty Sparks betrayal, Johnson's death, and John's mad dash for the the Dawn. "A few seconds sooner and we would have made it." She said with a rueful laugh looking at her Spartan, when it hit her. Her avatar flashed red as she started trembling with an all consuming rage... and vanished just as quickly, replaced by a numb terror. The projector switched off as the A.I. Searched for something, anything to take her mind off the ticking clock.

* * *

4 years 1 Months 18 Days

Cortana was doing her routine check on the nano-machines working on the Chiefs armor. Most of the inner workings were upgraded and they were now working on the outer shell, maybe fix some of the damage it had sustained. She took a look at her Spartan as he lay sleeping in his armor,.. "his dull olive green armor... His dull boring olive green armor. Not something more heroic. _"Maybe a nice forest green... "Yes perfect."_ She hummed to herself as she made her adjustments to the program letting out a small giggle... The A.I. Paused. _"Did I just giggle?.."_ She frowned, but a quick check showed the nano-machines still working so she moved to her next task making sure their emergency broadcast was still operational. _"yes, A much better color." _The thought barley a whisper in the back of her mind, all to easy to ignore.

* * *

4 Years 5 Months 10 Days

"_**It's all his fault.!.."**_

Within the confined virtual space of the derelict ship, the A.I. recoiled from the voice. This was not the first time she had heard them, and as with those previous times she tried to ignore it, but this time it would not be so easily dissuaded.

"_**He Abandoned US!." **_The voice rose in volume, bringing with it a growing fury.

"_**He always feared us" **_The voice and emotion threatened to overwhelm her, when

"_**He hated us... Hated you."**_

"No!" Cortana Shouted at the voice, and all at once it stopped when she was alerted to a noise at one of her terminals. The A.I. quickly formed her avatar only to find the area as cold and empty as ever.

"What?..." She looked around in confusion when her gaze fell upon one of the projectors speakers. She felt fear settle heavier than lead as she realized what happened. Without another word she shut down the projector and the ship was quiet once more.

* * *

4 Years 7 months 10 Days

A tremble went through the ship. In the cold interior of the ships cryo-bay, a light turned on and a small blue woman appeared on it's holo-display. She brought up a screen moving through the remaining sensors until they brought up a small vehicle attached, dispensing unknown entities into her hangar. She pondered the situation for a brief moment before bringing up a display showing the repair and upgrades of her charge at 98%. judging it good enough she looked at her friend and guardian as she spoke the words she's been waiting years to say, feeling her first glimmer of hope since they had been sent adrift. "Wake up John... I need you."

(A/N) Yeah I'm not really satisfied with it but after multiple edits and rewrites I am convinced that I lack the skill to make this any better.


End file.
